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James B. FlaneganDepartment Chair
Linda BloomAssociate Chair
Jörg BungertGraduate CoordinatorBMS/BMB [email protected]
Matthew MerrittAssociate Graduate CoordinatorBMS/BMBCGRC [email protected]
Molecular Biology Structural Biology
Metabolomics
https://biomed.med.ufl.edu/about/biochemistry-and-molecular-biology/
http://biochem.med.ufl.edu/
Biochemistry and Molecular Biology Concentration
Entering first-year students who are recruited by BMB but who plan to rotate with faculty in both BMB as well as other concentrations, will enroll in the GMS 6001 core course during the Fall semester of their first year. This will allow “undeclared students” to select either a BMB faculty mentor or a mentor in a different concentration after completing their three first-year rotation projects.
Entering first-year students who “declare” BMB as their Advanced Concentration, will have the option of taking a menu of BMB graduate courses instead of GMS 6001 during the Fall semester of their first year. This option will also apply to “declared BMB students” who are committed to work with a specific BMB faculty mentor (e.g., Fast Track students).
Undeclared, Declared, and Fast-Track Students
Biochemistry and Molecular Biology Concentration
First YearFall – “Undeclared”
students•“Core Course” (GMS 6001)
– 5 credits•Lab Rotation (GMS 6090) –
2 credit•Essentials of Graduate Research & Professional
Development (GMS 6003) -1 credit
•Journal Club (BCH 6936) -1 credit
Fall – “Declared” BMB students
•Eukaryotic Molecular Biology and Genetics (BCH
5413) – 3 credits•Graduate Course (Elective)
3 credits•Essentials of Graduate Research & Professional
Development (GMS 6003) 1 credit
•Lab Rotations (GMS 6090) – 1 credits
•Journal Club (BCH 6936) –1 credit
Spring – All BMB Students•Advanced Courses – 6
credits•Lab Rotations (GMS 6090)
– 1 credits•Responsible Conduct of
Biomedical Research (GMS 7003) – 1 credit
•Journal Club (BCH 6936) –1 credit
https://biomed.med.ufl.edu/about/biochemistry-and-
molecular-biology/
https://biomed.med.ufl.edu/about/biochemistry-and-molecular-biology/
Biochemistry and Molecular Biology Concentration
Requirements After the First Year:
Formal coursework:1. After completing the courses required in the Fall semester of the first year, a total of 12 credits of graduate courses at the 6000 level and above must be taken.2. Typically, 6 of those 12 credits are taken in the Spring semester of the first year, and the remaining 6 credits are taken in the second year.3. At least 4of the 12 credits must be BMB Advanced Courses (BCH prefix), and at least 3 credits must be from another concentration.
BMB Journal Club (BCH 6936) – 1 credit each Fall and Spring semesterBiochemistry Research Discussion (BCH 6040) – 1 credit each Fall and Spring semester
Qualifying Exam will be taken by November 1st of the third year.
Supervised Research–Successful completion of a Ph.D. degree requires students to carry out an independent research project, write a dissertation describing this work and defend the work in a public presentation.
Supervisory Committee– By the end of the first year, students must form a supervisory committee composed of 5 faculty members including the research mentor who serves as chair of the committee. In addition to the chair/research mentor, the committee must include 2 faculty members from the BMB concentration and an external member from outside the BMB concentration.
Supervisory Committee Meetings – After passing the qualifying exam, students have regular meetings (twice a year) with members of their supervisory committees.
Biochemistry and Molecular Biology Concentration
Three Curriculum Tracks:1. Metabolism and Metabolomics2. Molecular Biology3. Structural Biology
You can design your own course of study by mixing courses from the different tracks
Biochemistry and Molecular Biology Concentration
Metabolism LabsDr. Robert Cousins – Zinc metabolismDr. Susan Frost – Cancer microenvironment (CA IX)Dr. Tim Garrett – Clinical applications in mass spectrometryDr. Michael Kilberg – Nutrient stress responseDr. Joanna Long – Membrane structure and functionDr. Jianrong Lu – Hypoxia and Warburg effect in cancerDr. Matthew Merritt – Metabolism, stable isotope tracing, magnetic
resonance, and hyperpolarization
Biochemistry and Molecular Biology Concentration
Metabolism Labs
Metabolism Courses offered within the BMB Concentration
BCH6206 Metabolic Control Analysis, Fall semesterBCH6207 Adv. Metabolism: Role of Membranes in Signal Transduction
and Metabolic ControlBCH6208 Adv. Metabolism: Regulation of Key Reactions in
Carbohydrate and Lipid MetabolismBCH6209 Adv. Metabolism: Regulation of Key Reactions in Amino Acid
and Nucleotide MetabolismOthers:BCH6107 Biophysical Techniques in Proteomics, Spring semester
EM(cryo), Metabolomics etcBCH6876 Recent Advances in Membrane Biology Journal Club
Biochemistry and Molecular Biology ConcentrationMolecular Biology Labs
Dr. Bert Flanegan – RNA virus replicationDr. Mingyi Xie – Gene expression regulation by non-coding RNAs; microRNA biogenesisDr. Melike Caglayan- Genome integrity, DNA damage repair Dr. Linda Bloom – DNA replication, DNA damage repairDr. Michael Kilberg – Nutrient stress responseDr. Thomas Yang – Epigenetic alterations in fetal alcohol syndromeDr. Susan Frost – Cancer microenvironment (CA IX)Dr. John Dame - Molecular biology of the malaria parasiteDr. Jorg Bungert – Transcriptional control of the globin locusDr. Kevin Brown – Signaling controlling genome stabilityDr. Michael Kladde - Regulation of transcription by chromatinDr. Jianrong Lu – Transcriptional and epigenetic control of EMTDr. Michelle Gumz – Circadian clock function (kidney)Dr. Gregory Schultz – Ocular wound healingDr. Jon Licht – Aberrant gene regulation during hematopoiesisDr. Brian Cain – Membrane ATPases and endothelin gene regulation
Biochemistry and Molecular Biology Concentration
Molecular Biology Labs
BCH5413 Eukaryotic Molecular Biology and GeneticsBCH6415 Advanced Molecular and Cell BiologyBCH7410 Advanced Gene RegulationBCH7412 Epigenetics of Human Disease and DevelopmentBCH7414 Advanced Chromatin Structure
Epigenetics Journal Club
Molecular Biology Courses offered within the BMB Concentration
Structural Biology LabsDr. Mavis Agbandje-McKenna – ssDNA viruses
Dr. Linda Bloom – DNA repair/replication
Dr. Mathew Merritt - Metabolism, stable isotope tracing, magnetic resonance, and hyperpolarization
Dr. Joanna Long – Membrane proteins
Dr. Thomas Mareci – Mapping central nervous system
Dr. Robert McKenna – Proteins/enzyme structures
Collaborative studies
Biochemistry and Molecular Biology Concentration
Biochemistry and Molecular Biology ConcentrationStructural Biology Labs
X-ray, EM, CRYO-EMNMR, BIC, and National Facilities:
Structural Biology Courses offered within the BMB Concentration
BCH6740 Structural Biochemistry, Spring semesterBCH6744 Molecular Structure Determination by X-Ray CrystallographyBCH6741 Magnetic Resonance Imaging in Living SystemsBCH6745 Molecular Structure and Dynamics by NMR Spectroscopy
Others:BCH6749 Numerical Methods in Structural Biology, Summer semesterBCH6107 Biophysical Techniques in Proteomics, Spring semester
EM(cryo), Metabolomics etc
Center of Structural Biology Seminar Series
Crystallography and cryo-electron microscopy Journal Club
Biochemistry Journal Club (Tues 11:45am) – research and current literature – student invited speaker
Faculty Research Presentations(Wed 4:00pm) – B&MB and invited Faculty
Qualifying exam
Proposal – in the form of an NRSA predoctoral fellowship application (6 pages).
Several of our students have successfully obtained competitive external fellowships (NIH, NSF, AHA and private foundations). Proposal writing course – Dr. Bloom.
Courses offered within the BMB Concentration
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Mingyi Xie, PhDAssistant Professor
Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites.Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M.Nucleic Acids Res. 2018 Jun 20;46(11):5737-5752. doi: 10.1093/nar/gky306.
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Melike Caglayan, PhDAssistant Professor
Oxidized nucleotide insertion by pol β confounds ligation during base excision repair.Çağlayan M, Horton JK, Dai DP, Stefanick DF, Wilson SH.Nat Commun. 2017 Jan 9;8:14045. doi: 10.1038/ncomms14045
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Matthew Merritt, PhDAssociate Professor
A novel inhibitor of pyruvate dehydrogenase kinase stimulates myocardial carbohydrate oxidation in diet-induced obesity.Wu CY, Satapati S, Gui W, Wynn RM, Sharma G, Lou M, Qi X, Burgess SC, Malloy C, Khemtong C, Sherry AD, Chuang DT, Merritt ME.J Biol Chem. 2018 Jun 22;293(25):9604-9613. doi: 10.1074/jbc.RA118.002838. Epub 2018 May 8
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Linda Bloom, PhDProfessor and Associate Chair
Mechanism of opening a sliding clamp.Douma, L.G., Yu, K.K., England, J.K., Levitus, M. and Bloom, L.B. (2017) Nucleic Acids Res. 45, 10178-10189.
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Robert McKenna, PhDProfessor
"To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and SimulationKovalevsky, A, Aggarwal, M, Velazquez, H., Cuneo, M.J., Blakeley, M.P., Weiss, K.L., Smith, J.C., Fisher, S.Z., McKenna, R.(March 2018) Structure 26, 383–390
Biochemistry and Molecular Biology Concentration
BMB faculty who might take students next year
Joanna Long, PhDProfessor
Entropic Anomaly Observed in Lipid Polymorphisms Induced by Surfactant Peptide SP-B(1–25)Tran, N., Kurian, J., Bhatt, A., McKenna, R. and Long, J.R.(Sept 2017) J. Phys. Chem. B, 2017, 121 (39), pp 9102–9112
Biochemistry and Molecular Biology Concentration
Previous Students
Kristen Solocinski, Post-doctoral Fellow at the National Cancer Institute
Brian Mahon, Post-doctoral Fellow at Princeton University
Shweta Kailasan, Integrated Biotherapeutics
Biochemistry and Molecular Biology Concentration
Bala VenkatakrishmanSyngene International Limited, Contract Research Organization Bangalore, India
Karen Vieira, CEO of The Med Writers
Farzaneh Tondenevis, Automation Scientist atAdvanced Cell Diagnostics-Biotechne
Previous Students
Department of Biochemistry and Molecular BiologyCollege of Medicine(https://biochem.med.ufl.edu)
Alumni Spotlight: Joeva Barrow“I look forward to the next generation of brilliant scientists the Biochemistry Department will produce in the future.”
This month’s featured alumni is Dr. Joeva Barrow, a 2013 graduate of Dr. Jörg Bungert’s labratory, who is an assistant professor of Molecular Nutrition and Biochemistry at Cornell University. Her primary responsibilities are to maintain a successful extramurally-funded research program as well as to teach graduate level courses in Nutrition and Biochemistry.
Dr. Barrow’s research program centers around mitochondrial biology with a specific focus on mitochondrial disease and associated metabolic disorders such as obesity. We use unbiased high throughput discovery platforms such as small molecule and genome-wide CRISPR editing screens to identify and characterize novel regulatory factors that can be leveraged towards the treatment of metabolic disease.
Joeva describes her educational experience within the Department of Biochemistry and Molecular Biology at UF as being “paramount to my success. The combination of rigorous coursework, in addition to the advanced laboratory techniques and mentoring that I received from the laboratory of Dr. Jörg Bungert, has shaped me into the scientist that I am today. Ever since receiving the Boyce Research Competition award from the Biochemistry department in 2012, I have strived to achieve the level of excellence that is expected from our Biochemistry alumni. Now many years later, I am still very proud to have come from arguably the best department (!!) in the BMS program.”
Joeva says she lives “happily in Ithaca, New York, with my husband (also a UF alum) and our two children. We miss and think of UF often, especially when it is cold and snowing here! I look forward to the next generation of brilliant scientists the Biochemistry Department will produce in the future.”
Page 1 of 1Alumni Spotlight: Joeva Barrow » Department of Biochemistry and Molecular Biology » College...
8/9/2019https://biochem.med.ufl.edu/2019/01/01/alumni-spotlight-joeva-barrow/
Department of Biochemistry and Molecular BiologyCollege of Medicine(https://biochem.med.ufl.edu)
Alumni Spotlight: Mayank AggarwalDr. Mayank Aggarwal is a 2013 UF Department of Biochemistry and Molecular Biology graduate of Dr. Rob McKenna’s lab where his primary research focused on the structure-based drug design towards carbonic anhydrase inhibition.
Dr. Aggarwal is currently employed as a product manager and application scientist at Formulatrix, Inc. in Bedford, Massachusetts. Here at Formulatrix, Mayank manages two separate teams, each developing two different software systems, Rock Maker and Rock Imager, which are used in research labs that utilize their company’s protein crystallization automation solutions. Regarding his responsibilities, Mayank states, “My major responsibilities entail collecting customer feedback, prioritizing various new features, defining specific requirements for development by the software engineers, and ensuring their implementation in both software systems. I’ve been releasing at least two newer versions for
each of the systems every year. In addition, I also provide online and on-site trainings to customers within and outside the United States.”
Upon graduation in 2013, Mayank received the Shull Fellow award and went to work as an independent scientist at the Oak Ridge National Laboratory in Oak Ridge, Tennessee. In June of 2017, he made the transition from the Oak Ridge National Laboratory to Formulatrix, Inc.
With regards to the impact of the Department’s contribution to preparing Mayank for his career path, he states, “The beauty of the BMB department is not that it helps you achieve your desired path, but it prepares you to achieve whatever you may desire at whichever phase of your life. I say that because most students don’t know what the future holds for them, they just like to go with the flow and take up the usual Ph.D. academic postdoc path, hoping to one day become an assistant professor. But with experience and maturity, as one’s mind becomes more informed, desires change.”
Page 1 of 2Alumni Spotlight: Mayank Aggarwal » Department of Biochemistry and Molecular Biology » Co...
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Dr. Aggarwal also says that his career path has taken him from a Ph.D. student to a non-postdoc position of an independent scientist at a national lab (which he ways was amazing and scary at the same time), to a non-research position in industry. He says…
“It wouldn’t be incorrect to say that I had the opportunity to taste different waters. The knowledge and exposure provided by various highly qualified and helpful professors, journal clubs, seminars, and symposiums at the BMB has helped in an enormous way to develop character within me. It’s hard to quantify how much it has helped me, but it is impossible to imagine my present without my past in the BMB.”
Mayank grew up in the city of Delhi, India. He reflects that “I was always a city boy but 10 years of living in small towns in the US changed me completely. Even though it’s been a year since I moved to the Boston area, I’m still not used to the traffic and fast-paced life. My wife, Malvika, and I have a 3.5-year-old son, Parth, and he’s as naughty as a boy of his age could be; however, I’m told he did NOT get this from me.”
Page 2 of 2Alumni Spotlight: Mayank Aggarwal » Department of Biochemistry and Molecular Biology » Co...
8/12/2019https://biochem.med.ufl.edu/2018/11/09/alumni-spotlight-mayank-aggarwal/
Department of Biochemistry and Molecular BiologyCollege of Medicine(https://biochem.med.ufl.edu)
Alumni Spotlight: Zoë FisherDr. Zoë Fisher is currently the group leader for the Deuteration and Macromolecular Crystallization (DEMAX) platform at the European Spallation Source (ESS). Since 2016, she has held an adjunct position as Senior Lecturer at Lund University (Department of Biology) and since 2017 has also served as Deputy Division Leader for the Scientific Activities Division at ESS. DEMAX is a user support lab that focuses on chemical and biological deuteration, as well as support for large crystal growth. Prior to ESS Dr. Fisher was
a Research Scientist II in the Bioscience Division of Los Alamos National Laboratory. During this time, she served as the instrument scientist and also coordinated the user program for both the Protein Crystallography Station (PCS) instrument and user support labs at Los Alamos National Laboratory. Outside of her core duties related to the ESS, she is also engaged in collaborative research on the structure-function of carbonic anhydrases, biodeuteration strategies, neutron-based drug design, and large crystal growth for neutron studies.
Zoë grew up in South Africa and in 2000 completed her bachelor’s degree in Animal Physiology and Biochemistry at the University of Stellenbosch. At that time she traveled to the US and joined the lab of Prof. Chris West in the Anatomy and Cell Biology Department at UF. Here is how she describes her experience at UF: “It was to be a life changing decision as Prof. West encouraged me to take the GRE and apply for the IPD program at UF. In the first year I rotated through the lab of Prof. Robert McKenna and loved the lab atmosphere and learned a lot about protein structure-function through X-ray crystallography. The course work, lab work, and how the PhD program is structured in the Biochemistry Department taught me critical thinking skills, how to present my own and other’s research, and how to design experiments to answer fundamental questions about how enzymes work.”
“Five years ago my family and I decided to make the giant leap from the USA to Sweden so that I could join the European Spallation Source (ESS). At the heart of the ESS is a multi-country collaboration that is working together to build the world’s
brightest neutron source. The ESS is being constructed in Lund, Sweden and will support research in a wide range of scientific areas, from energy materials to drug design. Our DEMAX support lab is an integral part of user support and we provide a range of deuterated materials, from small
Page 1 of 3Alumni Spotlight: Zoë Fisher » Department of Biochemistry and Molecular Biology » College of...
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Zoë and son, Owen, handling a (non-venomous) snake at Le Bonheur crocodile farm outside of Stellenbosch, South Africa.
organic molecules to large proteins, and support for large protein crystal growth. Our users come from all over the world from the neutron research areas in chemistry, materials, life sciences, and soft matter.”
Regarding their transition from the USA to Sweden, Zoë states, “life is very different in Sweden than in my native South Africa and adopted home, the USA. I am married to a wonderful and supportive guy and we have a 10-year-old son, Owen. He was only 5 years old when we moved to Sweden and was a real trouper – adapting to a new school system and learning Swedish in a few months. My husband also took the dramatic move in stride and was very fortunate to find an excellent job close to home. We love life in the far north and the proximity to the rest of Europe. We travel a lot and that is probably our biggest hobby! This year we will visited a lot of new (and old) places, including spending the midsummer holiday above the arctic circle in Tromsø, Norway. We will also trek significantly further south and spend both Easter and Christmas in L’Agulhas – the southern tip of the African continent.”
In summary, Dr. Fisher states…
“the experiences and opportunities that UF and the Biochemistry Department gave me have set me up with right training and tools for my current adventure and whatever else life may bring in the future.”
Page 2 of 3Alumni Spotlight: Zoë Fisher » Department of Biochemistry and Molecular Biology » College of...
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The Fisher-Miles Family on the short of Lake Váttern, Sweden during a road trip Summer 2018
Page 3 of 3Alumni Spotlight: Zoë Fisher » Department of Biochemistry and Molecular Biology » College of...
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James B. FlaneganDepartment Chair
Linda BloomAssociate Chair
Jörg BungertGraduate CoordinatorBMS/BMB [email protected]
Matthew MerrittAssociate Graduate CoordinatorBMS/BMBCGRC [email protected]
Molecular Biology Structural Biology
Metabolomics
https://biomed.med.ufl.edu/about/biochemistry-and-molecular-biology/
http://biochem.med.ufl.edu/
